RNAbor statistics
RNAbor specifications
Information
Unique identifier | OMICS_05298 |
---|---|
Name | RNAbor |
Interface | Web user interface |
Restrictions to use | None |
Input data | RNA sequence, optionally a secondary structure for the input sequence |
Input format | FASTA |
Computer skills | Basic |
Stability | Stable |
Maintained | Yes |
Maintainer
- person_outline Peter Clote <>
Publication for RNAbor
RNAbor in publications
(6)Capturing alternative secondary structures of RNA by decomposition of base pairing probabilities
[…] for rna secondary structures, algorithms and tools that calculate the probability distribution of the secondary structures over the hamming distance from the reference structure has been proposed (rnabor [, ], rintd []). if the distribution is concentrated near to the reference structure, the structure is regarded as reliable (i.e. low credibility limit). if there are multiple clusters […]
[…] structure rules as described above, including a minimum length of hairpins of 3. the number of possible neighbours is bounded by o(n 2), where n is the length of the structure. the implementation rnabor for studying statistics of rna structural neighbours has been introduced in []. rnabor computes the number and boltzmann probabilities of all structures having base pair distance d to an input […]
An Efficient Minimum Free Energy Structure Based Search Method for Riboswitch Identification Based on Inverse RNA Folding
[…] such as in phmm [] and the advanced infernal, which also incorporates covariance models [–]. other approaches include boltzmann probability of rna structural neighbors for riboswitch detection as in rnabor []. genome-wide measurement of rna secondary structure by high-throughput sequencing [] can also be useful in attempting riboswitch discovery. on the topic of searching for new riboswitches […]
Efficient calculation of exact probability distributions of integer features on RNA secondary structures
[…] practical problems. the first example is the distribution of the hamming distances from a reference structure. a practically equivalent algorithm and its acceleration have been implemented as rnabor by [] and [], while we have reconstructed the algorithm by deducing from our general principle. the second example is the exact distributions of 5ʹ - 3ʹ distance. conventional methods […]
Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches
[…] to predict the location of riboswitch expression platform candidates. a web server is available at http://bioinformatics.bc.edu/clotelab/fftbor/., in , we developed a dynamic programming algorithm, rnabor, pronounced rna neighbor, which simultaneously computes for each integer , the boltzmann probability of the subensemble of structures whose base pair distance to a given initial, […]
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